Contacts of the helix formed by residues 48 - 69 (chain B) in PDB entry 3HAD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 48 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B THR* 1.3 73.0 + - - +
49B ASP* 1.3 60.0 + - - +
51B LEU* 3.1 19.7 + - - +
52B ALA* 2.6 39.3 + - - +
90B THR* 4.7 5.9 + - - -
91B SER* 5.5 1.6 + - - -
92B THR* 3.8 20.1 + - + +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 3.3 12.6 + - + +
48B GLU* 1.3 80.0 - - - +
50B ILE* 1.3 63.8 + - + +
52B ALA* 3.3 6.3 + - - +
53B LYS* 3.0 41.2 + - - +
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 3.3 38.8 - - + +
46B GLN* 4.6 6.7 - - + +
47B THR* 2.9 33.0 - - + +
49B ASP* 1.3 78.1 - - + +
51B LEU* 1.3 60.1 + - - +
53B LYS* 3.1 10.2 + - - +
54B SER* 2.8 37.4 + - - +
750B NAD 3.7 18.4 - - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY* 5.6 0.4 - - - -
43B LEU* 3.6 35.6 - - + +
44B VAL 4.0 2.0 - - - -
45B ASP* 3.6 26.7 - - + +
47B THR 3.0 9.9 + - - +
48B GLU* 3.5 28.0 - - - +
50B ILE* 1.3 77.0 - - - +
52B ALA* 1.3 63.4 + - - +
54B SER* 3.1 6.4 + - - +
55B LYS* 2.9 26.5 + - - +
90B THR* 4.0 16.2 - - + +
91B SER 3.4 33.0 - - - +
92B THR* 3.7 11.4 - - + -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU 2.6 20.8 + - - +
49B ASP* 3.5 9.4 - - - +
51B LEU* 1.3 72.5 - - - +
53B LYS* 1.3 64.1 + - + +
55B LYS* 3.6 4.7 + - - +
56B LYS* 3.2 22.2 + - - +
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP* 3.0 26.1 + - - +
50B ILE* 3.6 7.6 - - - +
52B ALA* 1.3 76.7 - - + +
54B SER* 1.3 66.1 + - - +
56B LYS* 3.2 11.2 + - + +
57B GLY* 3.0 21.0 + - - -
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY* 2.8 31.8 + - - -
28B ALA* 4.4 6.6 - - - +
43B LEU* 4.1 17.5 - - - -
50B ILE* 2.8 23.1 + - - +
51B LEU* 3.1 9.3 + - - -
53B LYS* 1.3 77.8 - - - +
55B LYS* 1.3 62.3 + - - +
57B GLY* 3.3 3.3 + - - -
58B ILE* 3.1 28.1 + - - +
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 5.0 2.0 - - + +
51B LEU 2.9 15.2 + - - +
52B ALA* 4.1 4.7 - - - +
54B SER* 1.3 77.7 - - - +
56B LYS* 1.3 62.9 + - - +
58B ILE* 3.3 13.0 + - + +
59B GLU* 3.0 22.5 + - - +
85B LEU* 3.5 37.1 + - + +
86B SER* 5.3 1.6 - - - +
88B ILE* 2.9 37.7 + - + -
89B ALA* 5.1 0.2 - - - +
90B THR* 4.2 21.0 - - + +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA 3.2 17.6 + - - +
53B LYS* 3.5 11.4 - - + +
54B SER 3.1 0.6 - - - -
55B LYS* 1.3 75.3 - - - +
57B GLY* 1.3 65.0 + - - +
59B GLU* 3.2 12.6 + - + +
60B GLU* 3.0 51.1 + - + +
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Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 6.2 0.7 - - - -
53B LYS 3.0 14.5 + - - -
54B SER* 3.3 3.6 + - - -
56B LYS* 1.3 76.4 - - - +
58B ILE* 1.3 61.8 + - - +
60B GLU* 3.4 13.5 + - - +
61B SER* 3.0 24.3 + - - -
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 3.7 36.3 - - + +
31B ALA* 4.2 8.3 - - + -
32B GLN* 3.7 29.2 - - + +
43B LEU* 4.5 7.9 - - + -
54B SER 3.1 17.1 + - - +
55B LYS* 3.5 15.7 - - + +
56B LYS 3.1 0.2 - - - -
57B GLY* 1.3 75.2 - - - +
59B GLU* 1.3 65.7 + - - +
61B SER* 3.3 2.8 + - - -
62B LEU* 2.9 37.8 + - + +
85B LEU* 4.3 4.5 - - + -
88B ILE* 4.2 27.1 - - + -
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LYS 3.0 13.8 + - - +
56B LYS* 3.6 14.7 - - - +
58B ILE* 1.3 76.1 - - - +
60B GLU* 1.3 61.5 + - + +
62B LEU* 3.2 2.3 + - - +
63B ARG* 2.8 67.0 + - + +
85B LEU* 3.8 31.3 - - + +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LYS* 3.0 48.8 + - + +
57B GLY* 3.6 10.7 - - - +
58B ILE 3.2 0.2 - - - -
59B GLU* 1.3 78.6 - - + +
61B SER* 1.3 56.9 + - - +
63B ARG* 3.2 7.6 + - - +
64B LYS* 2.8 31.6 + - - +
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 3.1 31.3 + - - -
57B GLY 3.0 14.1 + - - -
58B ILE 3.7 0.2 - - - -
60B GLU* 1.3 77.4 - - - +
62B LEU* 1.3 62.4 + - - +
64B LYS* 3.5 9.5 + - - +
65B VAL* 3.2 26.7 + - - +
164B PRO* 4.7 8.0 - - - +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 3.6 29.8 - - + +
36B ALA* 4.9 7.9 - - + -
58B ILE* 2.9 27.5 + - + +
59B GLU 3.6 3.1 - - - +
61B SER* 1.3 76.0 - - - +
63B ARG* 1.3 64.5 + - - +
65B VAL* 3.1 9.3 + - + +
66B ALA* 2.9 21.7 + - - +
80B PHE* 4.9 14.4 - - + -
81B VAL* 4.2 14.9 - - + +
84B THR* 3.4 32.1 - - + -
85B LEU* 3.2 31.4 - - + -
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 2.8 53.0 + - - +
60B GLU* 3.7 6.5 - - - +
62B LEU* 1.3 70.7 - - - +
64B LYS* 1.3 67.0 + - - +
65B VAL 3.0 0.2 + - - -
66B ALA* 3.1 2.1 + - - +
67B LYS* 2.9 43.8 + - + +
78B ASP* 3.0 32.5 + - - +
81B VAL* 3.9 35.0 - - + +
82B GLU* 5.5 2.2 - - - +
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU 2.8 18.2 + - - +
61B SER* 3.6 11.0 - - - +
62B LEU 3.3 0.2 - - - -
63B ARG* 1.3 75.3 - - - +
65B VAL* 1.3 63.5 + - + +
67B LYS* 4.0 8.7 + - - +
68B LYS* 3.6 44.3 - - - +
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 5.5 2.2 - - - +
61B SER* 3.2 20.6 - - - +
62B LEU* 3.1 8.9 + - + +
63B ARG 3.0 0.6 - - - -
64B LYS* 1.3 79.3 - - + +
66B ALA* 1.3 66.7 + - - +
68B LYS* 2.9 20.5 + - - +
69B LYS* 3.0 25.2 + - + -
80B PHE* 6.1 6.1 - - + -
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU 2.9 15.4 + - - +
63B ARG* 3.1 4.5 + - - +
65B VAL* 1.3 77.4 - - - +
67B LYS* 1.3 59.4 + - + +
69B LYS* 4.7 0.2 - - - -
70B PHE* 2.6 53.9 + - + +
77B GLY* 3.9 14.6 - - - +
80B PHE* 5.1 4.9 - - + -
81B VAL* 3.7 23.1 - - + -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 2.9 35.9 + - + +
64B LYS* 4.0 7.9 - - - +
66B ALA* 1.3 77.5 - - + +
68B LYS* 1.3 61.2 + - + +
70B PHE 5.4 0.7 - - - -
71B ALA* 3.8 20.4 + - - +
74B PRO* 5.5 7.9 - - - +
78B ASP* 4.5 17.2 + - - -
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS* 3.6 45.7 - - - +
65B VAL* 2.9 8.1 + - - +
67B LYS* 1.3 80.4 - - + +
69B LYS* 1.3 63.2 + - - +
70B PHE 3.4 0.4 + - - -
71B ALA* 3.7 14.1 + - - +
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.0 24.9 + - + +
66B ALA* 4.7 0.9 - - - -
68B LYS* 1.3 80.5 - - - +
70B PHE* 1.3 81.8 + - + +
71B ALA 3.4 1.2 + - - -
72B GLU 5.3 0.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il